Biodegradation of an oil is an alteration phenomenon caused by the oxidation of certain hydrocarbon molecules by micro-organisms or bacterial flora, which leads to the formation of a heavy oil, therefore difficult to produce and not very cost-effective commercially. The bacteria consume these molecules as they respire and to get the elements essential for their growth and their replication. The study of this phenomenon arouses renewed interest with the development of deep-sea exploration, the presence of heavy oil being a major risk. There are not many means currently available to predict biodegradation risks and to describe this phenomenon, whereas the economic need for the development of quantitative tools is great nowadays.
Biodegradation is a bio-geochemical process similar to a cold combustion performed by micro-organisms. A bacterium capable of degrading hydrocarbon compounds can in fact be considered as a hydrocarbon-consuming machine using electron acceptor ions (that can be compared to an oxidizer) and rejecting reducers.
A first condition for the existence of biodegradation is naturally the existence of these microorganisms. They are present in the medium either since the deposition of the sediment layer at the surface or because they have been brought there by meteoric water. In the absence of petroleum organic matter or of other sources of carbon (CO2, carbonate ions, etc.), the bacteria encyst and can be preserved during very long periods of time.
It is well-known that there are two distinct bacterial mechanisms causing the degradation of organic matter:                Catabolism, also referred to as respiration. It is the process of decomposition of the organic matter by oxidation in order to supply energy stored in the ATP (adenosine triphosphate) molecules. It requires organic matter and electron acceptor (not necessarily oxygen). The chemical balance is not yet well known and changes for each hydrocarbon molecule.        Anabolism. It is the process of formation of cellular matter allowing bacterial replication and growth. The bacterium needs all the constituent elements thereof, mainly C, O, N, S, K, P. Knowledge of the proportions of each of these elements in a bacterium would give a first balance of their relative consumption in the medium. Anabolism uses the energy supplied by respiration to effect its chemical reactions. The global chemical balance of a bacterium effecting its anabolism is thus a combination of the one related to the creation of cellular matter and of respiration.        
Respiration is a permanent process whereas anabolism occurs only at certain points in the life of the bacterium. Only respiration has been studied because it is considered to be preponderant over anabolism in the degradation of hydrocarbons. However, the two mechanisms are not independent. When a bacterium effects its anabolic process, it increases its respiration because it needs much energy.
The table hereafter gives examples of electron sources and acceptors, and of products of the reactions that can be observed in oil reservoirs.
Electron acceptorsElectron sourcesProductsO2HCCO2MnO2HC, H+CO2, Mn2+NO3−HC, H+CO2, N2Fe(OH)3HC, H+CO2, Fe2+SO42−HC, HC+CO2, H2SPossible CO2HCCO2, CH4
A known biodegradation model of a field from data from the Gullfaks field in the North Sea is described in the following publication:                Horstad I., Larter S. R., Mills N., A quantitative model of biological petroleum degradation within the Brent group reservoir, Org. Geochem., 19, pp. 107-117.        
According to this model, filling of a trap with hydrocarbons is considered with a constant flow. Water saturated with electron acceptors also circulates with a constant flow. The field has a simple parallelepipedic symmetry. During filling in the transition zone, the destruction of four n-alkanes is calculated by means of conventional kinetic laws of the first order obtained in the laboratory. The equational balance consists of a kinetic term of hydrocarbon destruction and the terms of hydrocarbon and electron acceptor supply by convection. The degradation is double, aerobic and by sulfate reduction.
In this system, the electron acceptor supply is the limiting factor. The parameters controlling the system are the thickness of the transition zone, the flow rate of water under the transition zone. The results obtained by this type of model are not really realistic. This is due to the balances and to the reaction kinetics selected, the latter being linked with the lack of knowledge about the bacterial kinetics and the attack mechanisms developed by the bacteria.
Models involving a more complex approach of the porous medium and of matter transport are commonly used to simulate biodegradation in shallow polluted layers. The SIMUSCOP model is notably used, which allows 2D-gridding of a subsoil and calculation of the aerobic biodegradation on the BTEX, developed by the applicant, on the basis of the work described in the publication hereafter:                Côme J. M., Expérimentation et modélisation de procédés in situ de dépollution par biodégradation aérobie des aquifères contaminés par des hydrocarbures, mémoire de thèse, pp. 75-93, April 95.        
The softwares BIO1D, developed by the ECHOSCAN company, RT3D or PARSSIM1 (Texas University) can also be mentioned. Documentation relative to these models is available at the following Internet addresses:                Model BIO1D: http://people.becon.org/˜echoscan/13-22 htm        Model PARSSIM: http://king.ticam.utexas.edu/Groups/SubSurfMod/ColorPictures/caption.html        Model RT3D: http://bioprocess.pnl.gov/rt3d_descrip.htm.        
A bibliography concerning the simulation of biodegradation within the framework of depollution is also available at the following address:                http://www.nal.usda.gov/wqic/Bibliographies/qb9406.html.        
In most of these models, only the hydrocarbon molecules with a high solubility in water (BTEX) are considered. Oil is therefore present in the dissolved form and moves only by diffusion. Sometimes, residual oil moving by convection is also taken into account. Although the oil saturations involved are not the same as in an oil reservoir and emphasis is put on matter transport in the aquifer, the mathematical problematics is in fact applicable to reservoirs.
The equations used in all these models are of the form as follows:
                                          ∂                          c              α                                            ∂            t                          =                                            ∂                              ∂                xi                                      ⁢                          (                                                Vc                  α                                -                                  D                  ⁢                                                            ∂                                              c                        α                                                                                    ∂                      xi                                                                                  )                                +                                    q              α                        ⁢                          c              α                                                          (        1        )            
In this equation, where
            ∂      c        ⁢                  ⁢    α        ∂    t  is an accumulation term, Vcα is a transport term,
  D  ⁢                    ∂        c            ⁢                          ⁢      α              ∂      xi      is a reaction term of the 1st order and qαcα is a source term,
T is time,
xi is a space variable at x, y and z,
P is the number of chemical species,
V(xi,t) is the velocity field of a fluid (water),
D(xi,t) is the diffusion coefficient,
cα is the concentration of species α, and
qα is the kinetic reaction coefficient of the 1st order of species α.
The problem is completed by means of a certain number of initial conditions and of boundary conditions such as the initial concentrations, the diffusion source zones, the impossible transport zones, etc.
In order to describe a geologic porous medium, 3D models have been developed wherein an aquifer zone is gridded, and the velocity fields and the concentrations are determined in each grid cell.
All these models provide a very realistic description of the geologic medium, but they only take into account oils whose composition is not very elaborate, limited to some molecules among the most soluble ones or even to a single type hydrocarbon molecule. These models are therefore not usable per se for modeling biodegradation in reservoirs in order to obtain a description of the evolution of oil. Furthermore, for an application to geologic time scales, the problem remains the type of kinetics applied for biodegradation reactions.